Thanks Jason,
These are both good options; I had thought of adding up the energies, but
was hoping for a simpler solution. " -e mden" provides this, which I
shouldn't have overlooked... (in fact, I had thought of using -e mden
now...).
You are right, this was for energy minimizations.
Thanks,
Marc
On 14 May 2012 13:52, Jason Swails <jason.swails.gmail.com> wrote:
> There are a couple options. You can simply have a script that adds up all
> of the other energy components (since each component goes up to 4 decimals,
> you'll have a final energy that goes up to 4 decimals as well).
>
> Alternatively, look at the "ntwe" variable and the "-e mden" output file
> flags, which provides a detailed energy printout every "ntwe" steps, and
> that should have much higher precision.
>
> You should also note that I've only really seen this as a problem for
> minimizations. In all dynamics simulations, you get printouts that contain
> the total potential and kinetic energies (as well as their sum, if I'm not
> mistaken). Therefore, only for minimizations will you be stuck in the
> dilemma of having to choose between using "ntwe" to print out detailed
> energy analysis or adding up every energy component to get 4 decimals of
> precision in the total energy.
>
> HTH,
> Jason
>
> On Mon, May 14, 2012 at 1:53 AM, Marc van der Kamp <
> marcvanderkamp.gmail.com
> > wrote:
>
> > Hi all,
> >
> > This may be a silly question, but in the manual or mailing list I
> couldn't
> > find a simple way to print out the total energy of the system with sander
> > with higher precision than given under "ENERGY" in the output (e.g. for
> > minimization).
> > The value under "ENERGY" is always in the scientific notification with 5
> > significant numbers (e.g. -1.2345E+05).
> > I would like to have the number with higher precision, e.g. -123456.7890.
> > When nmropt is used, a value like this is printed under EAMBER, but only
> if
> > you have non-zero values for your restraint force. So, a work-around
> would
> > be to apply a very miniminal force to a distance of two ('uninmportant')
> > atoms. But this is not ideal.
> >
> > Is there not an option or flag to simply print out the high precision
> total
> > energy without such a work-around?
> >
> > Thanks and apologies if I've overlooked something...
> > Marc
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon May 14 2012 - 06:00:08 PDT
